Contacts of the helix formed by residues 15 - 23 (chain B) in PDB entry 1HLG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B NAG 1.5 59.1 + - - +
13B THR 4.1 0.8 + - - -
14B MET* 1.3 74.5 - - - +
16B ILE* 1.3 66.4 + - - +
17B SER* 3.0 6.1 + - - -
18B GLN* 2.9 29.6 + - - -
19B MET* 3.0 23.6 + - - +
104B TRP* 3.1 30.9 - - + -
262B HIS* 4.7 1.3 - - - -
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 4.1 8.1 - - + -
15B ASN* 1.3 75.8 - - - +
17B SER* 1.3 65.8 + - - +
19B MET* 3.3 4.8 + - - +
20B ILE* 3.0 36.6 + - + +
43B ASN* 3.4 40.4 - - + +
71B ALA* 4.0 28.3 - - + +
72B THR* 3.8 29.4 - - + +
75B ILE* 4.9 2.2 - - + -
96B LEU* 4.1 17.3 - - + -
104B TRP* 3.5 25.8 - - + -
262B HIS* 5.3 0.2 - - - -
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B NAG 3.4 15.4 + - - +
15B ASN* 3.0 8.2 + - - -
16B ILE* 1.3 77.9 - - - +
18B GLN* 1.3 65.5 + - - +
20B ILE* 3.1 3.8 + - - +
21B THR* 3.0 30.3 + - - +
27B ASN* 3.4 23.8 + - - +
29B GLU* 2.7 27.2 + - - -
43B ASN* 3.5 8.0 + - - -
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Residues in contact with GLN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 3.3 38.9 + - - -
13B THR 4.3 2.8 - - - +
14B MET* 3.3 29.3 - - + +
15B ASN* 2.9 30.6 + - - +
17B SER* 1.3 73.4 - - - +
19B MET* 1.3 60.7 + - - +
21B THR* 3.4 8.6 + - - -
22B TYR* 2.8 32.7 + - - +
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Residues in contact with MET 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU* 3.7 25.8 - - + +
14B MET* 3.7 21.5 - - + -
15B ASN 3.0 15.3 + - - +
16B ILE 3.5 7.0 - - - +
18B GLN* 1.3 76.8 - - - +
20B ILE* 1.3 63.6 + - - +
22B TYR* 3.3 15.1 - - - +
23B TRP* 3.4 15.4 + - - -
72B THR* 4.0 17.9 - - - -
75B ILE* 3.9 13.7 - - + +
76B SER* 3.9 28.5 - - - -
85B PHE* 5.0 2.0 - - - -
258B VAL* 4.0 19.7 - - + -
262B HIS* 3.6 27.6 - - + +
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 3.0 19.3 + - + +
17B SER 3.5 6.5 - - - +
19B MET* 1.3 77.0 - - - +
21B THR* 1.3 62.2 + - - +
23B TRP* 3.2 13.9 + - - +
25B TYR* 3.5 26.1 + - + +
26B PRO 3.6 23.3 - - - +
27B ASN* 3.3 27.4 - - + +
43B ASN* 4.7 2.2 - - + -
45B ILE* 3.8 26.2 - - + -
75B ILE* 3.6 19.3 - - + -
85B PHE* 4.2 7.1 - - + -
96B LEU* 4.2 17.0 - - + -
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Residues in contact with THR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER* 3.0 18.0 + - - +
18B GLN* 3.4 12.1 + - - -
20B ILE* 1.3 72.5 - - - +
22B TYR* 1.3 67.1 + - - +
23B TRP 3.1 0.2 - - - -
24B GLY* 2.9 14.7 + - - -
25B TYR 3.6 15.3 - - - +
27B ASN* 3.8 23.1 - - + +
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Residues in contact with TYR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 3.2 32.4 - - + +
11B GLU* 3.5 23.6 - - - -
14B MET* 3.9 21.3 - - + -
18B GLN 2.8 19.9 + - - +
19B MET 3.3 7.4 - - - +
21B THR* 1.3 79.0 + - - +
23B TRP* 1.3 94.3 - + - +
24B GLY 3.3 0.7 + - - -
2D NAG 5.1 8.0 + - - -
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Residues in contact with TRP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 3.4 32.8 + - - -
19B MET 3.4 21.3 - - - -
20B ILE 3.2 3.6 + - - +
21B THR 3.1 1.0 - - - -
22B TYR* 1.3 95.8 - + - +
24B GLY* 1.3 61.0 + - - +
25B TYR* 3.4 30.5 - - + -
49B LYS* 4.0 9.4 - - - +
75B ILE 4.8 0.8 + - - -
77B ASN 3.5 21.3 + - - -
78B LEU* 3.7 15.7 - - + -
79B PRO* 3.5 24.5 - - + +
85B PHE* 3.6 19.5 - + + -
255B ARG* 4.1 2.7 - - - -
2D NAG 3.7 32.8 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il